NeuroR

NeuroR is a collection of tools to repair morphologies.
There are presently three types of repair which are outlined below.

Sanitization

This is the process of sanitizing a morphological file. It currently:

• ensures it can be loaded with MorphIO
  
• raises if the morphology has no soma or of invalid format
  
• removes unifurcations
  
• set negative diameters to zero
  
• raises if the morphology has a neurite whose type changes along the way
  
• removes segments with near zero lengths (shorter than 1e-4)
  Note: more functionality may be added in the future
  

Cut plane repair

The cut plane repair aims at regrowing part of a morphologies that have been cut out when the cell has been experimentally sliced.
neuror cut-plane repair contains the collection of CLIs to perform this repair.
Additionally, there are CLIs for the cut plane detection and writing detected cut planes to JSON files:

• If the cut plane is aligned with one of the X, Y or Z axes, the cut plane detection can be done automatically with the CLIs:
  

neuror cut-plane file<br />
neuror cut-plane folder<br />
```<br />
*    If the cut plane is not one the X, Y or Z axes, the detection has to be performed through the helper web application that can be launched with the following CLI:<br />
    <br />
```<br />
neuror cut-plane hint<br />
```<br />
### Unravelling<br />
Unravelling is the action of “stretching” the cell that has been shrunk because of the dehydratation caused by the slicing.<br />
The unravelling CLI sub-group is:<br />
```<br />
neuror unravel<br />
```<br />
The unravelling algorithm can be described as follows:<br />
*    Segments are unravelled iteratively.<br />
    <br />
*    Each segment direction is replaced by the averaged direction in a sliding window around this segment.<br />
    <br />
*    The original segment length is preserved.<br />
    <br />
*    The start position of the new segment is the end of the latest unravelled segment.